Suggested in #60

• with A
• with B

• BED12 - #53
• VCF - #49

Thanks so much for providing this tool to the community! I am finding it much faster than the existing toolkits.
Would it be possible to provide support for the bed12 format? Additionally, would it be possible to extend functionality to additional bedtools intersect flags such as -wo?
For people working in the single-molecule sequencing space these additions would be massively helpful.

Thanks again!

• number of intervals
• interval size
• number of chr

Right now the default is to read everything in as BED3 unless providing an alternative format to the -T flag.

Ideally this should autodetermine the format to be the number of columns in the input and fall-back to BED3 if it fails to do so.

There should also be two flags for left format and right format in case this is necessary.

Not having lex sorting can lead to a bug in streaming methods

Need to be able to mix file formats (i.e. bed3, bed6, bed12) when provided as inputs to operations requiring 2 files.

Multiple Files

• closest
• intersect
• subtract

Single Files

• complement
• extend
• get_fasta
• merge
• sample
• sort

Can close #65 once done

Hi @noamteyssier,

This seems like a great potential tool, but my bed files tend to be very large, so it would be awesome if you would considered allowing for compressed input (maybe through https://github.com/luizirber/niffler) and multithreaded compression of the output (maybe through https://github.com/sstadick/gzp).

Thanks for considering!
Mitchell

This is an issue to track the development of implementing stranded methods

• Closest
• Extend
• Get Fasta
• Intersect
• Flank
• Merge
• Random
• Sort
• Subtract
• Window

Matching development of bedrs-0.2

• Convert all instances of Containers into static structs of IntervalContainer

• Convert all numeric instances of Bed3, Bed4, Bed6, Bed12 into bedrs structs

• Handle mixed file formats and combinatorics with dispatch methods

• #68

• #31

Streamable Methods

• Closest
• Complement
• Extend
• Intersect
• Subtract

Named Streamable Methods

• Closest
• Complement
• Extend
• Intersect
• Subtract

Hi Noam!

I'm running a lot of bedtools intersect commands that I would love to replace with gia, but I was relying on the information in the bed6 format being retained.

e.g. fileA.bed
chr1 29300 29400

e.g. fileB.bed
chr1 29301 29400 CTAACTTTCCTATCAT-1 41 +
chr1 29328 29427 CTAACTTTCCTATCAT-1 40 -

e.g. output I need with the cell barcode.
chr1 29301 29400 CTAACTTTCCTATCAT-1 41 +

In this case, would I need to use bedrs instead of gia & create an interval type with my additional field?
-- Amanda

Are there plans to also support VCFs?

For Bed-like files with a variable number of fields and no fixed structure

Try a naive implementation of the coverage subcommand

• intersect
• window
• closest
• coverage
• map
• genomecov
• merge
• cluster
• complement
• shift
• subtract
• slop
• flank
• sort
• random
• shuffle
• sample
• spacing
• unionbedg

I meant to do some testing on my own, but I may never get there. I'm one of the authors of BEDOPS. It is not easy to imagine a 6x or so improvement in runtimes, as these are linear (or n log n for sorting) time algorithms in bedops/closest-features utilities.

There are a couple of things that stand out to me in the bioarxiv paper. Mainly, timed tests are at most 1 second for the slowest tool which indicates very, very small inputs (Figures 1 and 2). If the trend held with large inputs, that would be far more interesting and impressive. Right now, the differences might be attributable to things that do not generalize beyond 1 second, for example.

The memory overhead shown for bedops (Figure 5) makes me think that they used the "megarow" build of BEDOPS. That build is meant for very large sequencing results (nanopore and pacbio). It scales to those much larger data at the cost of some small memory overhead but also considerable time overhead. It would be worth measuring time/memory against that larger build but also against the more popular (and default) build for utilities in BEDOPS.

You can use the switch-BEDOPS-binary-type utility to switch between typical (default) and megarow builds of utilities in BEDOPS.